Abstract
Weak protein interactions between ubiquitin and the ubiquitin-proteasome system (UPS) enzymes that mediate its covalent attachment to substrates serve to position ubiquitin for optimal catalytic transfer. We show that a small-molecule inhibitor of the E2 ubiquitin-conjugating enzyme Cdc34A, called CC0651, acts by trapping a weak interaction between ubiquitin and the E2 donor ubiquitin-binding site. A structure of the ternary CC0651-Cdc34A-ubiquitin complex reveals that the inhibitor engages a composite binding pocket formed from Cdc34A and ubiquitin. CC0651 also suppresses the spontaneous hydrolysis rate of the Cdc34A-ubiquitin thioester without decreasing the interaction between Cdc34A and the RING domain subunit of the E3 enzyme. Stabilization of the numerous other weak interactions between ubiquitin and UPS enzymes by small molecules may be a feasible strategy to selectively inhibit different UPS activities.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Amino Acids / chemistry*
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Amino Acids / pharmacology
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Binding Sites
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Biphenyl Compounds / chemistry*
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Biphenyl Compounds / pharmacology
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Coordination Complexes / chemistry
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Crystallography, X-Ray
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Enzyme Activation / drug effects
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Enzyme Inhibitors / pharmacology
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Inhibitory Concentration 50
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Models, Molecular
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Protein Binding
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Protein Stability / drug effects
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Small Molecule Libraries / pharmacology
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Ubiquitin / chemistry*
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Ubiquitin-Conjugating Enzymes / antagonists & inhibitors*
Substances
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5-(3',5'-dichlorobiphenyl-4-yl)-2,3-dihydroxy-4-(2-methoxyacetamido)pentanoic acid
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Amino Acids
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Biphenyl Compounds
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Coordination Complexes
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Enzyme Inhibitors
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Small Molecule Libraries
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Ubiquitin
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Ubiquitin-Conjugating Enzymes
Associated data
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PDB/4MDK
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PubChem-Substance/165246638
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PubChem-Substance/165246639
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PubChem-Substance/165246640
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PubChem-Substance/165246641
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PubChem-Substance/165246642
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PubChem-Substance/165246643